User: Dattatray Mongad

Reputation:
350
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Trusted
Location:
National Centre for Cell Science, Pune
Website:
http://www.nccs.res.in/
Twitter:
DattatrayMongad
Last seen:
8 months, 1 week ago
Joined:
4 years ago
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d************@gmail.com

Posts by Dattatray Mongad

<prev • 63 results • page 1 of 7 • next >
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Answer: A: Need help in BLASTP parameters (dbsize & searchsp)
... You can refer the for more information on effect of dbsize, searchsp and query length on blast results in **[SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters][1]**. But, I think you need not have to worry about dbsize parameter as it is used for calculating e-v ...
written 8 months ago by Dattatray Mongad350
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Answer: A: kmer counting for heterozygosity estimation
... First of all, if you investigate the quality of your forward and reverse reads, you will find the poor quality of reverse reads as compared to forward. So, when you calculate k-mers frequencies for both reads it will be different (and being just imaginary if you cluster forward and reverse reads on ...
written 8 months ago by Dattatray Mongad350
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Comment: C: Extract V3-V4 regions from 16s sequences
... For my work, I have used modified primers for V4 (515f-806r) region of 16S rRNA gene as mentioned in [Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys][1] -f GTGYCAGCMGCCGCGGTAA -r GGACTACNVGGGTWTCTAAT [1]: ...
written 9 months ago by Dattatray Mongad350
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Answer: A: how to download cazy database
... Don't know about cazy but I have used [dbCAN][1] which you can download also. [1]: http://bcb.unl.edu/dbCAN2/ ...
written 14 months ago by Dattatray Mongad350
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Answer: A: How To Extract The Core Genes From The Orthomcl Output File?
... Use this code [parseOrthoMCLOutput.py][1]. It will generate all core, accessory and uniq genes fasta files. [1]: https://github.com/drdee255/code-Util/blob/master/parseOrthoMCLOutput.py ...
written 14 months ago by Dattatray Mongad350
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Answer: A: what is the best method (normalization) to compare RNA-Seq samples from differen
... Yes you can do PCA using TPM values and TMM has been widely used as normalization technique for transcriptome data. You can use [DESeq2][1] [1]: https://bioconductor.org/packages/release/bioc/html/DESeq2.html ...
written 19 months ago by Dattatray Mongad350
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Answer: A: Can't make program in Python to read FASTA
... **use biopython:** from Bio import SeqIO for records in SeqIO.Parse("fastaFileName","fasta"): print( records.id ) print( records.seq ) ...
written 22 months ago by Dattatray Mongad350 • updated 22 months ago by h.mon31k
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Answer: A: compare expression between the same gene in different organisms?
... In simple words, your idea is to take APOE gene sequence and blast it against genomes of other organisms. Using some strict BLAST output cutoffs you will manage to get estimated copy numbers of gene but not the expression levels. For measuring expression you will need microarray or transcriptome or ...
written 22 months ago by Dattatray Mongad350
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Answer: A: Metabolic pathways from list of protein ID numbers
... The server or tool depend on your protein ids. If its UniProt ids, then you can use UniProt id conversion tool and convert them to KEGG ids. Then use KeggMapper to get the list of pathways involved. You can follow typical gene enrichmnet analysis also. ...
written 23 months ago by Dattatray Mongad350
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Answer: A: What is microbiome community structure?
... Core means, bacterial OTU/genera present in all samples or individuals. To do core microbiome analysis please see this [tutorial][1] [1]: https://microbiome.github.io/microbiome/Core.html ...
written 23 months ago by Dattatray Mongad350

Latest awards to Dattatray Mongad

Popular Question 14 months ago, created a question with more than 1,000 views. For Genome annotation to KEGG KO ids
Scholar 14 months ago, created an answer that has been accepted. For A: Amino Acid matrices freely downloadable url
Scholar 19 months ago, created an answer that has been accepted. For A: Amino Acid matrices freely downloadable url
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Amino Acid matrices freely downloadable url
Scholar 23 months ago, created an answer that has been accepted. For A: Amino Acid matrices freely downloadable url
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Amino Acid matrices freely downloadable url
Scholar 2.1 years ago, created an answer that has been accepted. For A: Extract specific fasta sequences from multiple multi-fasta files located in a di

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